date:20130605

On Wed, Jun 5, 2013 at 9:42 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
 Hi Sarah

 you need to install the rpy module:

 http://rpy.sourceforge.net/rpy.html


 As a warning: we have been struggling to get rpy to work with newer versions
 of R. In or experience in only works with R version 2.9 and older. Thanks to
 a recent effort of our sysadmin, we can now use it with 2.15 - which is
 good, but not great, as our default version of R is now 3.0

According to the rpy list, using the latest code from SVN
you should be able to get rpy v1 to work under R 3.0.1,
http://sourceforge.net/mailarchive/message.php?msg_id=30999482

 Although we haven't started to us it, I recommend using rpy2:

 http://rpy.sourceforge.net/rpy2.html

Indeed - rpy v1 is still being maintained in SVN, but
hasn't had an official release with these fixed for
over two years.

 Most tools have been refactored by John Chilton

 see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html

We're not making heavy use of rpy in Galaxy yet, but I
hope John's good work switching to rpy2 gets integrated
soon.

Peter
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Creating workflow which includes Multifile upload

On Wed, Jun 5, 2013 at 8:56 AM,  alex.khassa...@csiro.au wrote:
 Hi John,

 One more problem with multifile upload – when I display a workflow which
 includes multi upload tool, I get:

 Module workflow_run_mako:476 in render_row_for_param
  __M_writer(unicode(param.get_label()))
 AttributeError: 'UploadDataset' object has no attribute 'get_label'

 Ok, I see that UploadDataset class is derived from Group, not ToolParameter.
 So I tried to add get_label() to the Group class, which returns some string.
 But then I get:

 Module workflow_run_mako:476 in render_row_for_param
  __M_writer(unicode(param.get_label()))
 TypeError: 'str' object is not callable

 Here my knowledge of Galaxy ends and I need some help please.

Hi Alex,

I guess from the Python exception that you didn't create a method
called get_label, but a property or attribute perhaps? Try this at the
python prompt and you'll get the same TypeError:

 hello()
Traceback (most recent call last):
  File stdin, line 1, in module
TypeError: 'str' object is not callable

I would have added a get_label method to the class using something
like this:

class UploadDataset(...):

def get_label(self):
   return Uploaded stuff

Peter

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Error / import rpy module

2013-06-05 Thread Sarah Maman


Thanks a lot for these explantions,

I have downloded refactored tools (rpy2 is more suited to our R version).
Unfortunatly, galaxy still do not import rpy2 ..

Traceback (most recent call last):
 File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line 
6, in module
   import rpy2.robjects as robjects
ImportError: No module named rpy2.robjects


Moreover our rpy2 module is avalaible and listed in our python. Maybe a 
problem with Python ?


Thanks in advance,
Sarah

Hans-Rudolf Hotz a écrit :

Hi Sarah

you need to install the rpy module:

http://rpy.sourceforge.net/rpy.html


As a warning: we have been struggling to get rpy to work with newer 
versions of R. In or experience in only works with R version 2.9 and 
older. Thanks to a recent effort of our sysadmin, we can now use it 
with 2.15 - which is good, but not great, as our default version of R 
is now 3.0


Although we haven't started to us it, I recommend using rpy2:

http://rpy.sourceforge.net/rpy2.html

Most tools have been refactored by John Chilton

see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html


Regards, Hans-Rudolf




On 06/05/2013 10:19 AM, Sarah Maman wrote:

Hello,

Some Galaxy tools failed to import rpy module and displays the following
message:

Traceback (most recent call last):
  File
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py,
line 5, in module
from rpy import *
ImportError: No module named rpy


For instance, the tool Regrouping (tools/stats/grouping.py) have been
refactored in 2011 by Kanwei Li to use numpy instead of rpy. And this
tool runs on my local instance of Galaxy.
But I would like to be able use rpy module instead of refactor the
others tools.

Could you, please, help me to understand why the eggs ' import does not
allow the use of rpy module? How to debug these tools?

Thnaks in advance,
Sarah





--
 --*--
Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53 
--*--


___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Creating workflow which includes Multifile upload

2013-06-05 Thread Alex.Khassapov

Hi Peter,

Of course I added def get_label(self), as a matter of fact, I copied 
get_label() from ToolParameter class. That's why I'm a bit confused.  

The get_label function returns a string which is supposed to be displayed, but 
instead something is trying to execute it?

Best Regards,

Alex Khassapov

Software Engineer
CSIRO IMT

From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Wednesday, 5 June 2013 7:36 PM
To: Khassapov, Alex (CSIRO IMT, Clayton)
Cc: chil...@msi.umn.edu; galaxy-...@bx.psu.edu; NeCTAR Cloud Imaging Project 
Team
Subject: Re: [galaxy-dev] Creating workflow which includes Multifile upload

On Wed, Jun 5, 2013 at 8:56 AM,  alex.khassa...@csiro.au wrote:
 Hi John,

 One more problem with multifile upload – when I display a workflow which
 includes multi upload tool, I get:

 Module workflow_run_mako:476 in render_row_for_param
  __M_writer(unicode(param.get_label()))
 AttributeError: 'UploadDataset' object has no attribute 'get_label'

 Ok, I see that UploadDataset class is derived from Group, not ToolParameter.
 So I tried to add get_label() to the Group class, which returns some string.
 But then I get:

 Module workflow_run_mako:476 in render_row_for_param
  __M_writer(unicode(param.get_label()))
 TypeError: 'str' object is not callable

 Here my knowledge of Galaxy ends and I need some help please.

Hi Alex,

I guess from the Python exception that you didn't create a method
called get_label, but a property or attribute perhaps? Try this at the
python prompt and you'll get the same TypeError:

 hello()
Traceback (most recent call last):
  File stdin, line 1, in module
TypeError: 'str' object is not callable

I would have added a get_label method to the class using something
like this:

class UploadDataset(...):

def get_label(self):
   return Uploaded stuff

Peter

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Creating workflow which includes Multifile upload

On Wed, Jun 5, 2013 at 12:21 PM,  alex.khassa...@csiro.au wrote:
 Hi Peter,

 Of course I added def get_label(self), as a matter of fact, I copied 
 get_label() from ToolParameter class. That's why I'm a bit confused.

 The get_label function returns a string which is supposed to be displayed, 
 but instead something is trying to execute it?

 Best Regards,

 Alex Khassapov

That rules out the simple answer then, that's a shame :(

Is your change on bitbucket, or could you post a diff, which might
help others in reproducing the problem?

Peter
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Creating workflow which includes Multifile upload

If you don't have pull request 122 in your code base, you will want to add it:

https://bitbucket.org/galaxy/galaxy-central/pull-request/122/add-optional-upload-attribute-to-tool/diff

Then, all you need to do is add the attribute '
workflow_compatible=false ' to your top level tool XML element in
multi_upload.xml.

See most updated version as demonstration:
https://bitbucket.org/msiappdev/galaxy-extras/src/904fcbe55c7cd16a80f310bfd5c18c8d1d43cc04/tools/data_source/multi_upload.xml?at=stable

-John

On Wed, Jun 5, 2013 at 2:56 AM,  alex.khassa...@csiro.au wrote:
 Hi John,



 One more problem with multifile upload – when I display a workflow which
 includes multi upload tool, I get:



 Module workflow_run_mako:476 in render_row_for_param
  __M_writer(unicode(param.get_label()))
 AttributeError: 'UploadDataset' object has no attribute 'get_label'



 Ok, I see that UploadDataset class is derived from Group, not ToolParameter.
 So I tried to add get_label() to the Group class, which returns some string.
 But then I get:



 Module workflow_run_mako:476 in render_row_for_param
  __M_writer(unicode(param.get_label()))
 TypeError: 'str' object is not callable



 Here my knowledge of Galaxy ends and I need some help please.



 -Alex

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Error / import rpy module

Three quick comments on this thread:

- A real short-coming of my colleague JJ is that he doesn't possess a
tenth the ego that I do, so he doesn't care, but I think it is
important he gets credit. He did 85% of the work, and the harder 85%
at that, so they should be called the JJ changes.

- It is possible to get rpy working with newer versions of R (at least
3.0.0) because CloudBioLinux is configured this way and it seems to
work for me. (Not that there aren't other problems -
https://github.com/chapmanb/cloudbiolinux/commit/302072341696390dc1cf3ae1dd88a9c1ca35a4fa).
CloudBioLinux is configured to get its rpy packages here
http://watson.nci.nih.gov/cran_mirror/bin/linux/ubuntu/{precise,quantal}
which has versions compatible with R 3.0.0.

- Finally, an idea - Death to RPY - The BoF. Everyone with a stake
in this meets with laptops at the Galaxy conference together and we
divvy up the remaining tools to convert (hopefully one tool per
person). Every person is also assigned two of the existing converted
tools to retest and clean up. As they are completed they are given to
a core Galaxy developer (Nate, Dannon, Daniel, any volunteers?) to
collect, re-retest, and okay. The changes are then committed all
together at the end and the next Galaxy release contains no
dependencies on rpy.

These tools are not updated frequently, so the advantage of these all
being upgraded in one commit before being shipped off to the tool shed
is that an institution that is really stuck on rpy1 for whatever
reason can just undo that single commit and keep going with the old
tools indefinitely.

If anybody with commit access signs on I will be happy create a BoF
page and attend this.

Thanks,
-John

On Wed, Jun 5, 2013 at 4:23 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Jun 5, 2013 at 9:42 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Sarah

you need to install the rpy module:

http://rpy.sourceforge.net/rpy.html

As a warning: we have been struggling to get rpy to work with newer versions
of R. In or experience in only works with R version 2.9 and older. Thanks to
a recent effort of our sysadmin, we can now use it with 2.15 - which is
good, but not great, as our default version of R is now 3.0

According to the rpy list, using the latest code from SVN
you should be able to get rpy v1 to work under R 3.0.1,
http://sourceforge.net/mailarchive/message.php?msg_id=30999482

Although we haven't started to us it, I recommend using rpy2:

http://rpy.sourceforge.net/rpy2.html

Indeed - rpy v1 is still being maintained in SVN, but
hasn't had an official release with these fixed for
over two years.

Most tools have been refactored by John Chilton

see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html

We're not making heavy use of rpy in Galaxy yet, but I
hope John's good work switching to rpy2 gets integrated
soon.

Peter
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Error / import rpy module

On Wed, Jun 5, 2013 at 2:18 PM, John Chilton chil...@msi.umn.edu wrote:
Three quick comments on this thread:

If anybody with commit access signs on I will be happy create a BoF
page and attend this.

Thanks,
-John

If you all can pull that off in Oslo, great. Otherwise a piecewise
conversion seems a sensible plan B, where both rpy (v1) and rpy2
are installed and things are updated on a tool by tool basis.

The BoF group might also have some collective wisdom on how
to deal with the question of multiple versions of R/BioConductor
given this is important for reproducibility of many more complex
and rapidly developed R tools.

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Death to RPY - The BoF

2013-06-05 Thread Hans-Rudolf Hotz




On 06/05/2013 03:33 PM, Peter Cock wrote:

On Wed, Jun 5, 2013 at 2:18 PM, John Chilton chil...@msi.umn.edu wrote:


//


- Finally, an idea - Death to RPY - The BoF. Everyone with a stake
in this meets with laptops at the Galaxy conference together and we
divvy up the remaining tools to convert (hopefully one tool per
person). Every person is also assigned two of the existing converted
tools to retest and clean up. As they are completed they are given to
a core Galaxy developer (Nate, Dannon, Daniel, any volunteers?) to
collect, re-retest, and okay. The changes are then committed all
together at the end and the next Galaxy release contains no
dependencies on rpy.

These tools are not updated frequently, so the advantage of these all
being upgraded in one commit before being shipped off to the tool shed
is that an institution that is really stuck on rpy1 for whatever
reason can just undo that single commit and keep going with the old
tools indefinitely.

If anybody with commit access signs on I will be happy create a BoF
page and attend this.

Thanks,
-John


If you all can pull that off in Oslo, great. Otherwise a piecewise
conversion seems a sensible plan B, where both rpy (v1) and rpy2
are installed and things are updated on a tool by tool basis.

The BoF group might also have some collective wisdom on how
to deal with the question of multiple versions of R/BioConductor
given this is important for reproducibility of many more complex
and rapidly developed R tools.

Peter



I like the BoF suggestion, I am just afraid we will be too busy in Oslo 
to do it...we probably have to go for Peter's back-up plan. And, thank 
to JJ's efforts we are already well into the piecewise conversion.


As part of our current work to set up a new box for our Galaxy 
development server at the FMI, we will use the already converted tools. 
I'll keep you posted.


Regarding the question of multiple versions of R/BioConductor: we 
intend to keep them, and if necessary 'freeze' a tool...but we are 
looking for a better solution.


Regards, Hans-Rudolf





___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

2013-06-05 Thread Keilwagen, Jens

Hi Greg,

I just updated our instance:

hg pull
hg update
sh manage_db.sh upgrade

and checked the current version

parent: 9944:cea3ddf6cdda tip
 Update tag for stable_2013.06.03
Zweig: stable
Ãbernehme: 16 unbekannt (clean)
Aktualisiere: (aktuell)

Subsequently, I tried again   and it took a while, but it works. Thank you 
very much.

All the best, Jens

 -Ursprüngliche Nachricht-
 Von: Greg Von Kuster [mailto:g...@bx.psu.edu]
 Gesendet: Dienstag, 4. Juni 2013 15:58
 An: Keilwagen, Jens
 Cc: Galaxy Dev
 Betreff: Re: AW: [galaxy-dev] Internal Server Error during installation
 of ncbi_blast_plus

 Hi Jens,

 Thanks for the information, but it doesn't help determine what is
 causing this behavior in your environment.  It's strange that you have
 never installed the ncbi_blast_plus repository (so it is not currently
 in some error state), and yet you cannot install it.  I am not able to
 reproduce this behavior, so I have no idea of it's cause or how to
 resolve it.

 We just completed the latest Galaxy release yesterday, so when it is
 convenient perhaps you could update your Galaxy environment again,
 although I don't believe your Galaxy version is the issue either.

 Sorry to not be of much help here, but this is unusual behavior that
 has not been seen in the community, so it's unclear how to resolve it.

 Greg Von Kuster

 On Jun 4, 2013, at 9:47 AM, Keilwagen, Jens wrote:

  Hi Greg,
 
  Thanks a lot for your email.
  I hope, I did do not misunderstand something. We are trying to
 install ncbi_blast_plus from the Galaxy main tool shed. As we did
 not manage to install ncbi_blast_plus the where clause does not
 make sense to me. Hence, I omit it. Here is the result.
 
  mysql select id, name, owner,
  mysql installed_changeset_revision,changeset_revision, deleted,
  mysql status, error_message from tool_shed_repository;
  +++---+--
 ++-+---+---+
  | id | name   | owner |
 installed_changeset_revision | changeset_revision | deleted | status
 | error_message |
  +++---+--
 ++-+---+---+
  |  1 | cutadapt   | lparsons  | 2d6671b10919
 | 2d6671b10919   |   0 | Installed | NULL  |
  |  2 | mirdeep2_and_targetspy | nikhil-joshi  | 798fe7ba8b5e
 | 798fe7ba8b5e   |   0 | Installed | NULL  |
  |  3 | clustalomega   | clustalomega  | bc707542e5de
 | bc707542e5de   |   0 | Installed | NULL  |
  |  4 | head_and_tail  | xuebing   | 00dba791c4a2
 | 00dba791c4a2   |   0 | Installed | NULL  |
  |  5 | seq_match  | xuebing   | 3fd777932736
 | 3fd777932736   |   0 | Installed | NULL  |
  |  6 | dreme  | xuebing   | 83fb93488cad
 | 83fb93488cad   |   0 | Installed | NULL  |
  |  7 | velvet_toolsuite   | edward-kirton | 4afe13ac23b6
 | 4afe13ac23b6   |   0 | Installed | NULL  |
  |  8 | velvet_optimiser   | simon-gladman | 43c89d82a7d3
 | 43c89d82a7d3   |   0 | Installed | NULL  |
  |  9 | roche454_toolsuite | edward-kirton | 368a6ebebdde
 | 368a6ebebdde   |   0 | Installed | NULL  |
  | 10 | mira_assembler | peterjc   | 4266cccbb45a
 | 4266cccbb45a   |   0 | Installed | NULL  |
  | 11 | abyss_toolsuite| edward-kirton | 92636934a189
 | 92636934a189   |   0 | Installed | NULL  |
  | 12 | bwa_wrappers   | devteam   | 150b3fe44caa
 | 150b3fe44caa   |   0 | Installed | NULL  |
  | 13 | mafft  | dereeper  | d7a735d3625e
 | d7a735d3625e   |   0 | Installed | NULL  |
  | 14 | blast_datatypes| devteam   | b3a3ba0c1d47
 | b3a3ba0c1d47   |   0 | Installed | NULL  |
  | 15 | blast  | edward-kirton | f3ac34855f5e
 | f3ac34855f5e   |   0 | Installed | NULL  |
  | 16 | cdf_plot   | xuebing   | 900fd0a7428d
 | 900fd0a7428d   |   0 | Installed | NULL  |
  | 17 | plot_distribution  | ynewton   | f180c4ef9128
 | f180c4ef9128   |   0 | Installed | NULL  |
  +++---+--
 ++-+---+---+
 
  Does this help?
 
 
  Best regards, Jens
 
  -Ursprüngliche Nachricht-
  Von: Greg Von Kuster [mailto:g...@bx.psu.edu]
  Gesendet: Dienstag, 4. Juni 2013 15:29
  An: Keilwagen, Jens
  Cc: Galaxy Dev
  Betreff: Re: [galaxy-dev] Internal Server Error during installation
  of ncbi_blast_plus
 
  Hello Jens.
 
  What is the name of the repository you are trying to install from
 the
  tool shed?  Can you run the following sql in

Re: [galaxy-dev] Tool Visibility

Any ideas?

Thanks! 

On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

 Suppose a tool didn't have any kind of configuration and therefore didn't 
 need to be displayed in the Analyze Data part of Galaxy. Is there a way to 
 modify tool_conf.xml so that a particular tool is only displayed in the 
 Workflow editor? 
 
 Thanks! 
 
 Sincerely,
 Michael E. Cotterell
 
 Ph.D. Student in Computer Science, University of Georgia
 Instructor of Record, Graduate RA  TA, University of Georgia
 mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
 mepc...@uga.edu (mailto:mepc...@uga.edu)
 m...@cs.uga.edu (mailto:m...@cs.uga.edu)
 http://michaelcotterell.com/



___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Tool Visibility

 On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

 Suppose a tool didn't have any kind of configuration and therefore didn't
 need to be displayed in the Analyze Data part of Galaxy. Is there a way
 to modify tool_conf.xml so that a particular tool is only displayed in the
 Workflow editor?

 Thanks!

 Sincerely,
 Michael E. Cotterell

On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
 Any ideas?

 Thanks!

The only way this makes sense to me if is you have a tool with no inputs
at all (not even an input data file), but it produces one or more output files.
e.g. Fetch the human genome as FASTA file, version hg18. But in that
case you'd be better off just defining the file within a shared data library.

Perhaps you could give an example of the kind of tool you are interested in?

Thanks,

Peter
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails

2013-06-05 Thread Linda Cham



Hi.   I am new to the Galaxy forum and I am trying to setup a new local
Galaxy instance with MySQL on RH6.2 x86_64.

On a newly installed OS node, using the hg clone command (hg clone
https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current
Galaxy 20130603 image, I am getting the following errors when running
run.sh:
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in
execute
self.errorhandler(self, exc, value)
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
in key specification without a key length) 'CREATE INDEX ix_history_slug
ON history (slug)' ()

Reading the forum, someone stated it can be bypass by running the CREATE
INDEX.

mysql CREATE INDEX ix_history_slug ON history (slug(1000));
Query OK, 0 rows affected (0.09 sec)
Records: 0  Duplicates: 0  Warnings: 0

When trying to run.sh again after the CREATE INDEX, will get this error:
  File /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py, line
52, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get
( '__file__', None ), self.config.database_engine_options, app=self )
  File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
 line 107, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest,
config_arg ) )
Exception: Your database has version '29' but this code expects version
'115'.  Please backup your database and then migrate the schema by running
'sh manage_db.sh upgrade'.

So try to run the sh manage_db.sh upgrade' now will get this error:
$ sh manage_db.sh upgrade
Traceback (most recent call last):
  File ./scripts/manage_db.py, line 13, in module
from migrate.versioning.shell import main
  File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
 line 12, in module
from migrate.versioning import api
  File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
 line 33, in module
from migrate.versioning import (repository, schema, version,
  File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py,
 line 13, in module
from migrate.versioning import version, pathed, cfgparse
  File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py,
 line 10, in module
from migrate.versioning import pathed, script
  File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py,
 line 11, in module
from migrate.versioning.util import KeyedInstance
  File
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py,
 line 7, in module
from decorator import decorator
ImportError: No module named decorator

In some searches, there were tips of deleting the eggs directory and rerun
run.sh or use a python env.  Neither option worked.
Was not able to find anything meaningful about the decorator error.

Note:, I was able to get Galaxy up with MySQL using the Galaxy 788cd3d06541
image on a different node.  So I am thinking maybe it is the new 20130603
image that is giving me issues?

Commands used to get Galaxy up:
   Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1]
   python version [2.6.6]

   Grant ALL PRIVILEGES galaxy_db.* TO  galaxy_user on localhostname with
   PWD
   Images tested:


*Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image  Did not
   run the hg update command. [This worked]


*hg clone stable of newest image [Failed]


   Update the universe_wsg.ini with the port, host, database_connection to
   mysql


   Ran run.sh


Thanks.


Linda___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Tool Visibility

Peter,

Thanks for getting back to me.

I'm working on an existing project where my predecessors have added a tool that 
enables a user to add REST and SOAP Web services as usable tools within Galaxy 
by providing their WSDL or WADL URLs. It makes sense that the tools that are 
added should show up in both the Analyze page and the Workflow editor, but 
the actual tool for adding Web services is not intended to be used in workflows.

I understand that this tool should probably (more appropriately) be located on 
the Admin page, but in the short run, I'd like to hide this tool from showing 
up in the list of tools available in the Workflow editor (admittedly, this is 
the opposite of my original question).
In the long run, is there an API for adding plugins (or similar) to the admin 
page? I ask because this particular tool is not designed to be used in a 
workflow, but rather, it is designed to add tools to Galaxy itself.

Perhaps there is a way to work this into the Toolshed stuff you guys are 
working on?

Any thoughts are much appreciated.

Thanks! 

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA  TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/


On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:

  On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:
  
   Suppose a tool didn't have any kind of configuration and therefore didn't
   need to be displayed in the Analyze Data part of Galaxy. Is there a way
   to modify tool_conf.xml so that a particular tool is only displayed in the
   Workflow editor?
   
   Thanks!
   
   Sincerely,
   Michael E. Cotterell
  
 
 
 
 On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
 mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
  Any ideas?
  
  Thanks!
 
 The only way this makes sense to me if is you have a tool with no inputs
 at all (not even an input data file), but it produces one or more output 
 files.
 e.g. Fetch the human genome as FASTA file, version hg18. But in that
 case you'd be better off just defining the file within a shared data library.
 
 Perhaps you could give an example of the kind of tool you are interested in?
 
 Thanks,
 
 Peter 


___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails

2013-06-05 Thread Dannon Baker

Hi Linda,

The decorator issue should be resolved in galaxy-central now.  I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.

Thanks!

-Dannon


On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote:

 Hi.   I am new to the Galaxy forum and I am trying to setup a new local
 Galaxy instance with MySQL on RH6.2 x86_64.

 On a newly installed OS node, using the hg clone command (hg clone *
 https://bitbucket.org/galaxy/galaxy-dist#stable*https://bitbucket.org/galaxy/galaxy-dist)
 which gets the current Galaxy 20130603 image, I am getting the following
 errors when running run.sh:
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173,
 in execute
 self.errorhandler(self, exc, value)
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line
 36, in defaulterrorhandler
 raise errorclass, errorvalue
 OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
 in key specification without a key length) 'CREATE INDEX ix_history_slug
 ON history (slug)' ()

 Reading the forum, someone stated it can be bypass by running the CREATE
 INDEX.

 mysql CREATE INDEX ix_history_slug ON history (slug(1000));
 Query OK, 0 rows affected (0.09 sec)
 Records: 0  Duplicates: 0  Warnings: 0

 When trying to run.sh again after the CREATE INDEX, will get this error:
   File /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py,
 line 52, in __init__
 create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
 ).get( '__file__', None ), self.config.database_engine_options, app=self )
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
 line 107, in create_or_verify_database
 % ( db_schema.version, migrate_repository.versions.latest, config_arg
 ) )
 Exception: Your database has version '29' but this code expects version
 '115'.  Please backup your database and then migrate the schema by running
 'sh manage_db.sh upgrade'.

 So try to run the sh manage_db.sh upgrade' now will get this error:
 $ sh manage_db.sh upgrade
 Traceback (most recent call last):
   File ./scripts/manage_db.py, line 13, in module
 from migrate.versioning.shell import main
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
 line 12, in module
 from migrate.versioning import api
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
 line 33, in module
 from migrate.versioning import (repository, schema, version,
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py,
 line 13, in module
 from migrate.versioning import version, pathed, cfgparse
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py,
 line 10, in module
 from migrate.versioning import pathed, script
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py,
 line 11, in module
 from migrate.versioning.util import KeyedInstance
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py,
 line 7, in module
 from decorator import decorator
 ImportError: No module named decorator

 In some searches, there were tips of deleting the eggs directory and rerun
 run.sh or use a python env.  Neither option worked.
 Was not able to find anything meaningful about the decorator error.

 Note:, I was able to get Galaxy up with MySQL using the Galaxy
 788cd3d06541 image on a different node.  So I am thinking maybe it is the
 new 20130603 image that is giving me issues?

 Commands used to get Galaxy up:

Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1]
python version [2.6.6]

Grant ALL PRIVILEGES galaxy_db.* TO  galaxy_user on localhostname with
PWD
Images tested:

*Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image  Did not
run the hg update command. [This worked]

*hg clone stable of newest image [Failed]

Update the universe_wsg.ini with the port, host, database_connection
to mysql

Ran run.sh



 Thanks.

 Linda


 ___
 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

 To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search

Re: [galaxy-dev] Tool Visibility

Add workflow_ compatible =false to the tool XML element to hide it
in the workflow editor. Check the tools/data_source/upload.xml for an
example of this.

If you would like to hide it both in the workflow editor and the side
bar but still allow for other direct links to it you can setup dynamic
toolbox filters (you will need to manually pull in the pull request
changes as this has not been merged by the Galaxy team):

https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters

These can even let you show it to your admins in their side panel, but
not to other users. This way you don't have to hack up the admin
section of the UI.

Additionally, you may want to go one step further and prevent others
from using the tool (not just preventing them from seeing it). To do
this, you can use dynamic job destinations and prevent these tools
from running for non-admins:

http://wiki.galaxyproject.org/Admin/Config/Jobs

-John

On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
Peter,

Thanks for getting back to me.

I'm working on an existing project where my predecessors have added a tool
that enables a user to add REST and SOAP Web services as usable tools within
Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools
that are added should show up in both the Analyze page and the Workflow
editor, but the actual tool for adding Web services is not intended to be
used in workflows.

I understand that this tool should probably (more appropriately) be located
on the Admin page, but in the short run, I'd like to hide this tool from
showing up in the list of tools available in the Workflow editor (admittedly,
this is the opposite of my original question).
In the long run, is there an API for adding plugins (or similar) to the admin
page? I ask because this particular tool is not designed to be used in a
workflow, but rather, it is designed to add tools to Galaxy itself.

Perhaps there is a way to work this into the Toolshed stuff you guys are
working on?

Any thoughts are much appreciated.

Thanks!

Sincerely,
Michael E. Cotterell

Ph.D. Student in Computer Science, University of Georgia
Instructor of Record, Graduate RA TA, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/

On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:

On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

Suppose a tool didn't have any kind of configuration and therefore didn't
need to be displayed in the Analyze Data part of Galaxy. Is there a way
to modify tool_conf.xml so that a particular tool is only displayed in
the
Workflow editor?

Thanks!

Sincerely,
Michael E. Cotterell

On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Any ideas?

Thanks!

The only way this makes sense to me if is you have a tool with no inputs
at all (not even an input data file), but it produces one or more output
files.
e.g. Fetch the human genome as FASTA file, version hg18. But in that
case you'd be better off just defining the file within a shared data library.

Perhaps you could give an example of the kind of tool you are interested in?

Thanks,

Peter

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Tool Visibility

This is great! Will it work with sections as well?

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:

Add workflow_ compatible =false to the tool XML element to hide it
in the workflow editor. Check the tools/data_source/upload.xml for an
example of this.

https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters

These can even let you show it to your admins in their side panel, but
not to other users. This way you don't have to hack up the admin
section of the UI.

http://wiki.galaxyproject.org/Admin/Config/Jobs

-John

On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Peter,

Thanks for getting back to me.

I'm working on an existing project where my predecessors have added a tool
that enables a user to add REST and SOAP Web services as usable tools
within Galaxy by providing their WSDL or WADL URLs. It makes sense that the
tools that are added should show up in both the Analyze page and the
Workflow editor, but the actual tool for adding Web services is not
intended to be used in workflows.

I understand that this tool should probably (more appropriately) be located
on the Admin page, but in the short run, I'd like to hide this tool from
showing up in the list of tools available in the Workflow editor
(admittedly, this is the opposite of my original question).
In the long run, is there an API for adding plugins (or similar) to the
admin page? I ask because this particular tool is not designed to be used
in a workflow, but rather, it is designed to add tools to Galaxy itself.

Perhaps there is a way to work this into the Toolshed stuff you guys are
working on?

Any thoughts are much appreciated.

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:

On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

Suppose a tool didn't have any kind of configuration and therefore
didn't
need to be displayed in the Analyze Data part of Galaxy. Is there a
way
to modify tool_conf.xml so that a particular tool is only displayed
in the
Workflow editor?

Thanks!

Sincerely,
Michael E. Cotterell

On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Any ideas?

Thanks!

Perhaps you could give an example of the kind of tool you are interested
in?

Thanks,

Peter

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Tool Visibility

On Wed, Jun 5, 2013 at 4:37 PM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
 Peter,

 Thanks for getting back to me.

 I'm working on an existing project where my predecessors have added a tool 
 that enables a user to add REST and SOAP Web services as usable tools within 
 Galaxy by providing their WSDL or WADL URLs. It makes sense that the tools 
 that are added should show up in both the Analyze page and the Workflow 
 editor, but the actual tool for adding Web services is not intended to be 
 used in workflows.

 I understand that this tool should probably (more appropriately) be located 
 on the Admin page, but in the short run, I'd like to hide this tool from 
 showing up in the list of tools available in the Workflow editor (admittedly, 
 this is the opposite of my original question).
 In the long run, is there an API for adding plugins (or similar) to the admin 
 page? I ask because this particular tool is not designed to be used in a 
 workflow, but rather, it is designed to add tools to Galaxy itself.

 Perhaps there is a way to work this into the Toolshed stuff you guys are 
 working on?

 Any thoughts are much appreciated.

 Thanks!

 Sincerely,
 Michael E. Cotterell

I can see similarities to the part of the Tool Shed Factory program,
http://www.ncbi.nlm.nih.gov/pubmed/23024011

Peter

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Tool Visibility

Yes to the toolbox filters, no the dynamic job destinations (these
need to be configured per tool).

Look at the last example included with the pull request -
per_host_tool_sections for an example of how to configure tool section
filters.

-John

On Wed, Jun 5, 2013 at 10:51 AM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
This is great! Will it work with sections as well?

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:

Add workflow_ compatible =false to the tool XML element to hide it
in the workflow editor. Check the tools/data_source/upload.xml for an
example of this.

https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters

These can even let you show it to your admins in their side panel, but
not to other users. This way you don't have to hack up the admin
section of the UI.

http://wiki.galaxyproject.org/Admin/Config/Jobs

-John

On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Peter,

Thanks for getting back to me.

I'm working on an existing project where my predecessors have added a tool
that enables a user to add REST and SOAP Web services as usable tools
within Galaxy by providing their WSDL or WADL URLs. It makes sense that
the tools that are added should show up in both the Analyze page and the
Workflow editor, but the actual tool for adding Web services is not
intended to be used in workflows.

I understand that this tool should probably (more appropriately) be
located on the Admin page, but in the short run, I'd like to hide this
tool from showing up in the list of tools available in the Workflow editor
(admittedly, this is the opposite of my original question).
In the long run, is there an API for adding plugins (or similar) to the
admin page? I ask because this particular tool is not designed to be used
in a workflow, but rather, it is designed to add tools to Galaxy itself.

Perhaps there is a way to work this into the Toolshed stuff you guys are
working on?

Any thoughts are much appreciated.

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:

On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

Suppose a tool didn't have any kind of configuration and therefore
didn't
need to be displayed in the Analyze Data part of Galaxy. Is there
a way
to modify tool_conf.xml so that a particular tool is only displayed
in the
Workflow editor?

Thanks!

Sincerely,
Michael E. Cotterell

On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Any ideas?

Thanks!

Perhaps you could give an example of the kind of tool you are interested
in?

Thanks,

Peter

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists,

[galaxy-dev] error after pulling latest updates

2013-06-05 Thread Branden Timm


Hi All,
  Just did an update to HEAD, and upon restarting the daemons received 
the following messages:


galaxy.jobs.handler DEBUG 2013-06-05 10:55:31,478 recovering job 2083 in 
condor runner

Traceback (most recent call last):
  File 
/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, 
line 35, in app_factory

app = UniverseApplication( global_conf = global_conf, **kwargs )
  File /home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/app.py, line 
164, in __init__

self.job_manager = manager.JobManager( self )
  File 
/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/manager.py, line 
36, in __init__

self.job_handler.start()
  File 
/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 
34, in start

self.job_queue.start()
  File 
/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 
77, in start

self.__check_jobs_at_startup()
  File 
/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 
125, in __check_jobs_at_startup

self.dispatcher.recover( job, job_wrapper )
  File 
/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/handler.py, line 
620, in recover

self.job_runners[runner_name].recover( job, job_wrapper )
  File 
/home/GLBRCORG/galaxy/galaxy-central/lib/galaxy/jobs/runners/condor.py, line 
243, in recover
cjs.user_log = os.path.join( 
self.app.config.cluster_files_directory, '%s.condor.log' % galaxy_id_tag )

NameError: global name 'galaxy_id_tag' is not defined
Removing PID file main.pid

--
Branden Timm
bt...@energy.wisc.edu
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Tool Visibility

John,

Is there a way to hide an entire section (not just make it greyed out) using
the most recent galaxy-dist?

I'm investigating the pull request you linked to, and it looks interesting, but
is it compatible with galaxy-dist (it's on the bitbucket page for
galaxy-central)?

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:

Add workflow_ compatible =false to the tool XML element to hide it
in the workflow editor. Check the tools/data_source/upload.xml for an
example of this.

https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters

These can even let you show it to your admins in their side panel, but
not to other users. This way you don't have to hack up the admin
section of the UI.

http://wiki.galaxyproject.org/Admin/Config/Jobs

-John

On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Peter,

Thanks for getting back to me.

I'm working on an existing project where my predecessors have added a tool
that enables a user to add REST and SOAP Web services as usable tools
within Galaxy by providing their WSDL or WADL URLs. It makes sense that the
tools that are added should show up in both the Analyze page and the
Workflow editor, but the actual tool for adding Web services is not
intended to be used in workflows.

I understand that this tool should probably (more appropriately) be located
on the Admin page, but in the short run, I'd like to hide this tool from
showing up in the list of tools available in the Workflow editor
(admittedly, this is the opposite of my original question).
In the long run, is there an API for adding plugins (or similar) to the
admin page? I ask because this particular tool is not designed to be used
in a workflow, but rather, it is designed to add tools to Galaxy itself.

Perhaps there is a way to work this into the Toolshed stuff you guys are
working on?

Any thoughts are much appreciated.

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:

On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

Suppose a tool didn't have any kind of configuration and therefore
didn't
need to be displayed in the Analyze Data part of Galaxy. Is there a
way
to modify tool_conf.xml so that a particular tool is only displayed
in the
Workflow editor?

Thanks!

Sincerely,
Michael E. Cotterell

On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Any ideas?

Thanks!

Perhaps you could give an example of the kind of tool you are interested
in?

Thanks,

Peter

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy

Re: [galaxy-dev] Tool Visibility

If you look at the date on the pull request it looks like it was a
full month before they even froze central for the last dist release,
so at this point I would be more confident it is going to work with
galaxy-dist than galaxy-central.

-John

On Wed, Jun 5, 2013 at 11:04 AM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
John,

Is there a way to hide an entire section (not just make it greyed out) using
the most recent galaxy-dist?

I'm investigating the pull request you linked to, and it looks interesting,
but is it compatible with galaxy-dist (it's on the bitbucket page for
galaxy-central)?

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:49 AM, John Chilton wrote:

Add workflow_ compatible =false to the tool XML element to hide it
in the workflow editor. Check the tools/data_source/upload.xml for an
example of this.

https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dynamic-toolbox-filters

These can even let you show it to your admins in their side panel, but
not to other users. This way you don't have to hack up the admin
section of the UI.

http://wiki.galaxyproject.org/Admin/Config/Jobs

-John

On Wed, Jun 5, 2013 at 10:37 AM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Peter,

Thanks for getting back to me.

I'm working on an existing project where my predecessors have added a tool
that enables a user to add REST and SOAP Web services as usable tools
within Galaxy by providing their WSDL or WADL URLs. It makes sense that
the tools that are added should show up in both the Analyze page and the
Workflow editor, but the actual tool for adding Web services is not
intended to be used in workflows.

I understand that this tool should probably (more appropriately) be
located on the Admin page, but in the short run, I'd like to hide this
tool from showing up in the list of tools available in the Workflow editor
(admittedly, this is the opposite of my original question).
In the long run, is there an API for adding plugins (or similar) to the
admin page? I ask because this particular tool is not designed to be used
in a workflow, but rather, it is designed to add tools to Galaxy itself.

Perhaps there is a way to work this into the Toolshed stuff you guys are
working on?

Any thoughts are much appreciated.

Thanks!

Sincerely,
Michael E. Cotterell

On Wednesday, June 5, 2013 at 11:08 AM, Peter Cock wrote:

On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote:

Suppose a tool didn't have any kind of configuration and therefore
didn't
need to be displayed in the Analyze Data part of Galaxy. Is there
a way
to modify tool_conf.xml so that a particular tool is only displayed
in the
Workflow editor?

Thanks!

Sincerely,
Michael E. Cotterell

On Wed, Jun 5, 2013 at 4:02 PM, Michael E. Cotterell
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote:
Any ideas?

Thanks!

Perhaps you could give an example of the kind of tool you are interested
in?

Thanks,

Peter

___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

Re: [galaxy-dev] Tool Visibility